Table 3.

Summary of study characteristics, demographics, radiation type, sample collection and analysis, and main findings of the eligible studies in animals (except mice).

Animals	Author, Year / Interventional	Participants / N Irradiated	Microbiome Assessment Method / Type of Sample / Number of Samples	Main Findings
		Type of Radiation
Rats	Rentea RM, 2016 [36] / Interventional	Rats WAG/RijCmer Male 5 weeks / N = 15 5—Nonirradiated; 5—irradiated; 5—intestinal alkaline phosphatase (RT + IAP)	16s rRNA / Real-time PCR / Fecal N = 2 D0 and 4 days after irraiation	Composition Bacteroidetes—unaltered Firmicutes—slightly decreased Proteobacteria—greatly increased (100,000 xs)
		X-rays 13 Gy—single dose / Intestinal lower hemibody radiation
	Lam V, 2012 [37] / Interventional	Rats WAG/RijCmcr (Wistar) Male 5 weeks / N = 10 (n = 5/group)	qPCR and 16S rRNA / Second Genome Inc. G3 PhyloChipe 16S rRNA microarray-based assay / Fecal N = 4 D0 and days 4, 11, and 21 post-irradiation	Composition Proteobacteria increased almost 1000-fold 4 days after 10 Gy and then returned to control values. 18 Gy prolonged increase over 5 days compared to over 3 days observed after 10 Gy Bacteroidetes—less affected Cyanobacteria OTU 31,902 increased Clostridia—less affected Clostridia OTU 39,153 decreased OTU 42,924 unchanged Bacteroidales—increased Lactobacillaceae and Streptococcaceae—increased Peptostreptococcaceae—unchanged Clostridiaceae—unchanged abundance but 47 separate OTUs decreased
		X-rays TBI Single dose 10.0 Gy Multiple-fraction 18.0 Gy
Wild rodent: Bank Vole Myodes glareolus	Lavrinienko A, 2018 [38] / Observational	Wild rodent: Bank Vole Myodes glareolus / N = 137	16S rRNA V4 / Illumina MiSeq platform at BGI / Fecal	Diversity/richness Neither community richness nor evenness differed significantly (p > 0.05) between samples grouped by study area Significant differences in beta diversity Composition Radiation was identified as a significant predictor of the abundance of Bacteroidetes, Firmicutes and Proteobacteria (p = 0.001) ratio of Firmicutes to Bacteroidetes decreased Some members of the Desulfovibrionaceae can tolerate high radiation levels (CH) and have a potential for bioremediation of radionuclides
		3 study areas of environmental radiation: (1) high (CH) and (2) low (CL and KL)
	Lavrinienko, 2020 [39] / Observational	Wild rodent: Bank Vole Myodes glareolus / 28 individuals provided fecal (CL1 n = 3, CL2 n = 13; CH1 n = 8, CH2 n = 4). (84–43 Recapture)	16s rRNA V4 / Illumina MiSeq platform at BGI / Fecal N = 1	Diversity/richness alpha diversity (number of ASVs, Shannon Index) unchanged. Composition Enrichment of members of the S24-7 family (Bacteroidetes) in samples from CL and an increase in ASVs assigned to Ruminococcaceae, Lachnospiraceae (Firmicutes) and Desulfovibrionaceae families in CH samples. Second capture CL: S24-7 family (>10% reduction in relative abundance) decreased Ruminococcaceae and Lachnospiraceae (p < 0.05)—increased
		Ambient radiation Chernobyl High Radiation (CH) and Chernobyl Low radiation (CL)
Göttingen minipigs and Chinese rhesus macaques	Carbonero F, 2018 [40] / Interventional	Göttingen Minipigs and Chinese rhesus Macaques 8 Minipigs 8 Macaques	16s rRNA / Illumina MiSeq / Fecal N = 2 -2/3 days before -3 days after	Minipigs Diversity/richness Shannon index—decreased Composition Clostridiales—increased Bacteroides and Paraprevotella—decreased Blautia, Oscillibacter, Streptococcus and Lactobacillus—increased Roseburia, Ruminococcus and unclassified Lachnospiraceae—Significant decreased Macaques Diversity/richness No significant effect diversity indices (taxa number and Shannon index) Composition Verrucomicrobia increased unclassified Lachnospiraceae and Veillonellaceae—increased Both Helicobacter increased Treponema, Elusimicrobium increased
		6 MV linear accelerator (LINAC) 80 ± 2.5 Gy/min 1.8 Gy Minipigs 6.8 Gy Macaques
	Carbonero F, 2018 [41] / Interventional	Göttingen minipigs Chinese rhesus macaques / N = 74 male Chinese rhesus macaques 50 Minipigs	16s rRNA / Illumina MiSeq QIAGEN / Fecal / Minipigs: collected on days 0 and 3 Macaque fecal samples were collected 24 h before irradiation, between 1–3 h postirradiation and on days 3 and 14 postirradiation	Macaques Diversity/richness Overall diversity was not significantly affected Number of taxa observed decreased numerically (66 to 63) Composition Firmicutes decreased Spirochaetes increased Actinobacteria decreased Proteobacteria and Bacteroidetes—increased Helicobacter and Treponema—decreased/only higher radiation levels—immediate increase. Betaproteobacteria members, Desulfovibrio and Bilophila—decreased Streptococcus and Prevotella—decreased Bacteroides and Parabacteroides—increased Paraprevotella and Clostridium clusters IV and XIVa—increased Clostridium increased Clostridium XIVa Significant positive correlations Blautia and Lactobacillus increased Actinobacteria major genera—decrease (Collinsella and Slackia) Collinsella higher radiation levels were characterized by lower numbers Slackia higher radiation levels—lower numbers Minipigs Richness Number of genera—increased Composition Firmicutes and Verrumicrobia increased Bacteroidetes and Proteobacteria decreased Bacteroides, Clostridium, Roseburia—decreased Streptococcus increased Oscillibacter increased/correlated negatively with radiation intensity Blautia increased Elusimicrobium All radiation levels led to significant decreases/were found to correlate negatively with radiation intensity until 2.1 Gy. Prevotella, Faecalibacterium, Bifidobacterium decreased Clostridium cluster IV, XIVa and XIVb: High radiation levels (1.95–2.25 Gy) led to increases Olsenella and Alistipes—increased Butyricimonas and Collinsella—decreased Ruminococcus and Clostridium XIVa—significant positive correlations Lactobacillus correlate negatively
		Macaques 5.9 Gy (n = 12); 6.3 Gy (n = 14); 6.8 Gy (n = 16); 7.2 Gy (n = 16); and 7.7 Gy (n = 16) Minipigs 1.65 Gy (n = 9); 1.80 Gy (n = 10); 1.95 Gy (n = 11); 2.10 Gy (n = 13); and 2.25 Gy (n = 7)
Chinese rhesus macaques, Macaca mulatta	Kalkeri R, 2021 [42] / Interventional	Chinese rhesus macaques, Macaca Mulatta / N = 19	Fecal samples / N = 3 1 day prior and 1 and 4 days after exposure	Diversity/richness Alpha Diversity (Shannon Diversity Index) revealed no major difference between pre- and post-irradiation, Beta diversity analysis showed significant differences in the microbiome after irradiation (day + 4) compared to baseline (pre-irradiation) Composition Firmicutes/Bacteriodetes ratio—decreased Actinobacillus, Bacteroides, Prevotella (Paraprevotellaceae family) and Veillonella—significantly increased Acinetobacter and Aerococcus—decreased
		Gamma-rays 7.4 Gy
Flies	Cai Z, 2018 [43] / Interventional	Flies Males Bactrocera dorsalis 3000 pupae irradiated 15 guts irradiated 15 guts control	16s rRNA V4 / Illumina MiSeq QIIME v1.8 / Gut / Irradiation 48h before eclosion Day1 Day7 Day14 Post eclosion	Diversity/richness Diversity significant increase at 1 DPE (ACE, Chao1, Shannon indexes). At 7 DPE, the ACE, Chao1 and Shannon indexes increased Chao1 index—significant difference between irradiated and control flies, at 7 DPE. Richness increased Total bacteria decreased by 40% at 1 DPE. No significant differences at 7 or 14 DPE Composition Enterobacteriaceae decreased 54% at 1 DPE, 52% at 7 and 51% at 14 DPE Bacillaceae, Clostridiaceae, Xanthomonadaceae, Sphingobacteriaceae, Aeromonadacea and Flavobacteriaceae increased significantly
		100Gy gamma ray Gammacell 220 60Co With an activity of 9435 × 1015 Bq Central dose of 8Gy/min at the beginning of the test
	Ben Ami, 2020 [44] / Interventional	Flies Vienna 8 Wild C capitata pupae / 150 bacterial colonies from non irradiated 150 colonies from 5-day-old irradiated flies and 100 colonies from field flies	16s rRNA / PCR-DGGE	Diversity Gut bacterial diversity, as expressed by the total number of bands appearing in the gel, is reduced at eclosion day in the irradiated gut compared with non-irradiated guts and to those of 5-day-old males (3.47 ± 0.22 bands per lane for the irradiated eclosion day gut compared with 5.3 ± 0.39 and 5.55 ± 0.62 bands per lane for the non-irradiated eclosion day gut and 5-day-old gut, respectively) Composition Non-irradiated vs. irradiated vs. irradiated mass 5 day-read Klebsiella sp.—18.67% vs. 4.0% vs. 23.0%. Is a dominant community among the total gut microbiota of the non-irradiated, 5-day-old irradiated flies and of wild flies (18.67, 23.0, and 31.0%, respectively); its prevalence in the gut of the irradiated flies on eclosion day is significantly lower (4.0%, t-test: t ¼ 2.0129, p < 0.05) Enterobacter sp.—21.33% vs. 37.33% vs. 23.0% Citrobacter sp.—9.3% vs. 4,6% vs. 4.0% Bacillus sp.—8.0% vs. 7.33% vs. 2.0% Pseudomonas sp.—20.67% vs. 27.33% vs. 16.0% Ralstonia sp.—10.0% vs. 8.67% Providencia sp.—12.0% vs. 4.0% vs. 22.0%
		Delta irradiation
	Woruba DN [45] / Interventional	Flies Queensland fruit fly, Bactrocera Tryoni 54 = (3 × 18)	16S rRNA V3 and V4 regions QIIME / Intact gut dissections / N = 2 1 and 14 days after irradiation	Diversity/richness Diversity increased No changes in bacterial diversity and in relative abundance of OTU Bacterial load increased
		Delta irradiation